Add DMRfinder installation + documentation and test section

bismark_0.24.2.def

@@ -7,10 +7,11 @@ BootStrap: docker
 From: ubuntu:22.04
 
 %help 
-Description : This is a singularity/apptainer container packing bismark v0.24.2. It can be run by mounting a host bowtie2 installation directory, preferably towards /usr/bin/bowtie2/ destination to avoid PATH problems. Python2 is installed with the required librairies to run the miniconda version of bowtie2-2.3.2 present on the ccub.
-exemple : singularity exec -e --bind /work/gad/shared/bin/bowtie2-2.3.2/:/usr/bin/bowtie2[:options],<python2_directory>:/usr/bin/python/ <path/to/this/container.sif> bismark [--<options>] --genome <path/to/bismark/converted/genome> <fastq.file>
+Description : This is a singularity/apptainer container packing bismark v0.24.2. It can be run by mounting a host bowtie2 installation directory, preferably towards /usr/bin/bowtie2/ destination to avoid PATH problems. Python2 is installed with the required librairies to run a version of bowtie2 present on the ccub. DMRFinder is installed in /usr/bin/DMRfinder/ along with R v.4.4.0 and the bioconductor DSS package.
 Use "singularity test <path/to/this/container.sif>" to see --version calls of installed softwares.
 This container has no runscripts.
+Usage exemple : singularity exec -e --bind /work/gad/shared/bin/bowtie2-2.3.2/:/usr/bin/bowtie2 <path/to/this/container.sif> bismark [--<options>] --genome <path/to/bismark/converted/genome> <fastq.file>
+Usage exemple2 : singularity exec -e <path/to/this/container.sif> samtools view -h <bismark.output.bamfile>  |  python extract_CpG_data.py  -i -  -o <CpG.file.output.name>  -v
 Authors : valentin.vautrot@u-bourgogne.fr
 
 %post
@@ -21,11 +22,14 @@ apt-get install -y --no-install-recommends apt-utils
 apt-get install -y --no-install-recommends \
     locales \
     language-pack-fr \
+    software-properties-common \
+    dirmngr \
     wget \
     samtools \
     python2.7 \
     python2.7-dev \
-    libtbb2
+    libtbb2 \
+    git
 
 ln -s /usr/bin/python2.7 /usr/bin/python
 
@@ -57,6 +61,25 @@ rm -rf /usr/bin/bismark/
 # create mount directory for bowtie2 bind, to avoid problems
 mkdir /usr/bin/bowtie2
 
+# add DMRFinder scripts
+git clone https://github.com/jsh58/DMRfinder.git /usr/bin/DMRfinder/
+# correct DMRfinder bug
+sed -i 's/level <- levels(res\$chr)/level <- levels(as.factor(res\$chr))/' /usr/bin/DMRfinder/findDMRs.r 
+
+# Install R for DMRfinder and DSS Bioconductor package
+wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/"
+
+apt-get install -y --no-upgrade --no-install-recommends -t jammy-cran40 r-base-core=4.4.0-1.2204.0 r-base-dev=4.4.0-1.2204.0
+
+apt-get install -y --no-upgrade --no-install-recommends libcurl4-openssl-dev zlib1g-dev libxml2-dev libssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libbz2-dev gfortran
+
+echo "installed R version :"
+R --version
+
+# # install R packages :
+Rscript -e 'install.packages("BiocManager", dependencies=TRUE)'
+Rscript -e 'BiocManager::install("DSS", version = "3.19")'
 
 %environment
 export PATH=${PATH}:/usr/bin/samtools/:/usr/bin/Bismark-0.24.2/:/usr/bin/bowtie2/:/usr/bin/python:/usr/bin/python2.7:/usr/lib/x86_64-linux-gnu/:/usr/lib/python2.7/
@@ -71,9 +94,20 @@ samtools --version
 echo "############################"
 bismark --version
 echo "############################"
+echo "installed R version :"
+R --version
+echo "############################"
 echo "PATH variable : $PATH "
+echo "############################"
+echo "python version :"
+python --version
+echo "############################"
+echo "DMRfinder scripts versions :"
+python /usr/bin/DMRfinder/extract_CpG_data.py --version  
+python /usr/bin/DMRfinder/combine_CpG_sites.py --version
+Rscript /usr/bin/DMRfinder/findDMRs.r --version
 
 %labels
 Author valentin.vautrot
-container_version 0.1
+container_version 0.3
 Ubuntu_version 22.04
\ No newline at end of file